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    Mahendra Paipuri
    @mahendrapaipuri
    The API request URL is supposed to be https://galaxyhost/cos/api/histories/<snippet>. Am I missing any configuration or is it a bug?
    Mahendra Paipuri
    @mahendrapaipuri
    Seems like there was a similar issue here -> galaxyproject/galaxy#9970
    Marius
    @mvdbeek:matrix.org
    [m]
    Yes, can you open an issue ?
    Mahendra Paipuri
    @mahendrapaipuri
    Sure, I will! Cheers @mvdbeek:matrix.org
    Martin Wolstencroft
    @martinwolst:matrix.org
    [m]
    Hello, does anyone know why the toolshed tool revision number might not agree with that shown in the admin view in galaxy - even if the commit tag does match? e.g. for anndata_inspect my Galaxy says 286a24ac079c is revision 2, toolshed says it is revision 3
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    There was a minor update between revision 2 and 3, see https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=ead79880a5775ad3
    That means you can update your rev 2 to rev 3, but not have both revisions installed at the same time.
    because the tool version stayed the same (simplified version of "there was no change in repository metadata).
    Martin Wolstencroft
    @martinwolst:matrix.org
    [m]
    Thank you, that makes sense
    Helena
    @hexylena:matrix.org
    [m]

    We have some sad news to share, Simon Gladman (@slugger70) has passed away over the weekend. He was such an integral part of the Galaxy Admin community, especially admin training, sharing all of his knowledge from years of building, running, and scaling UseGalaxy.org.au.

    I don't remember where exactly I met him, but he's been a dear, dear friend for half a decade at this point, and together we've taught many years of admin training courses together. His absence will be felt keenly, especially for many of us in this community that learned a lot from him over the years. I have so many fond memories of working with him on Galaxy admin issues, he was such a bright and lively figure and will be missed.

    His colleagues have posted this in memoriam, and if you want to share your memories of him: https://www.biocommons.org.au/news/simon-gladman

    1 reply
    bwlang
    @bwlang:matrix.org
    [m]
    Thanks for sharing this sad news... he was a kindred spirit. Simon introduced me to King Gizzard and Lizard Wizard... https://www.youtube.com/watch?v=3pczVJvElyo seems fitting right now. I hope we can think of a project to honor him at the cofest.
    Helena
    @hexylena:matrix.org
    [m]
    ah he loved the Gizz, reckon he told everyone he met about them
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Yeah I suspect there are many a Gizz fan out there in the world thanks to him
    Nikolay Vazov
    @vazovn:matrix.org
    [m]
    I can't believe it - only a month ago we were drinking beer in Freiburg! He was so happy about the GCC in Brisbane and said with his inimitable humor : "It is going to be the first time a GCC will not cost me a fortune!"
    Morgan Ludwig
    @mjbludwig
    Does anyone have a working proxied reports webapp with a recent version of galaxy?
    still pointing to that blog post but that is based off of when galaxy was using ini files for config
    I think I am just missing how to set the prefix for the reports app properly since the following nginx config does redirect right, the scripts just 404:
            location ^~ /reports/ {
                    proxy_pass http://127.0.0.1:9001/;
                    proxy_set_header   X-Forwarded-Host $host;
                    proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
    
            }
    Morgan Ludwig
    @mjbludwig
    well I guess .ini is not deprecated but the docs should be updated for the yml version since that is default
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Yes, sorry about that, we need to update the documentation. It should work if you set SCRIPT_NAME like so: https://github.com/galaxyproject/galaxy/issues/14591#issuecomment-1284885084
    1 reply
    Lucille Delisle
    @lldelisle
    Dear admin experts,
    I wanted to try the upgrade from 22.01 to 22.05 on a VM before doing it for real. To make it as close as possible to my current instance, I wanted to restore the postgres database.
    I am currently using ansible roles on my instance and my postgres database is backed-up to a remote server with the PITR method (I think this is it as I used the ansible variable postgresql_backup_dir). So, I have my directory current with what I think is the last back up and I try to restore this backup on my VM. I tried to follow the procedure described here: https://www.postgresql.org/docs/12/continuous-archiving.html#BACKUP-PITR-RECOVERY but I don't understand it very well and I don't have a pg_wal directory. Did someone ever restore a database using this? Would you have the command lines?
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Here's the process I used in testing the updates to backup: https://github.com/galaxyproject/ansible-postgresql/pull/30#issuecomment-963600656
    Lucille Delisle
    @lldelisle
    Could you confirm that the 'data directory' is /var/lib/postgresql/13/main in your example?
    stop and start postgres is with systemctl right?
    Where do you 'set' the restore_command? I guess in the config file but I don't know where it is...
    1 reply
    Lucille Delisle
    @lldelisle
    Sorry, it seems that the recovery did not work. Could you spot what I did wrong?
    # I try to follow https://github.com/galaxyproject/ansible-postgresql/pull/30#issuecomment-963600656
    # Stop the server
    systemctl stop postgresql
    sudo systemctl status postgresql
    # ● postgresql.service - PostgreSQL RDBMS
    #      Loaded: loaded (/lib/systemd/system/postgresql.service; enabled; vendor preset: enabled)
    #      Active: inactive (dead) since Fri 2022-12-02 20:36:42 CET; 10s ago
    #     Process: 63683 ExecReload=/bin/true (code=exited, status=0/SUCCESS)
    #    Main PID: 62043 (code=exited, status=0/SUCCESS)
    
    # Dec 02 10:07:21 svvm0147 systemd[1]: Starting PostgreSQL RDBMS...
    # Dec 02 10:07:21 svvm0147 systemd[1]: Finished PostgreSQL RDBMS.
    # Dec 02 10:08:03 svvm0147 systemd[1]: Reloading PostgreSQL RDBMS.
    # Dec 02 10:08:03 svvm0147 systemd[1]: Reloaded PostgreSQL RDBMS.
    # Dec 02 20:36:42 svvm0147 systemd[1]: postgresql.service: Succeeded.
    # Dec 02 20:36:42 svvm0147 systemd[1]: Stopped PostgreSQL RDBMS.
    
    # Restore
    # Become postgres
    sudo su - postgres
    # Remove files:
    mkdir /tmp/test/
    mv /var/lib/postgresql/12/main/* /tmp/test/
    # Add backup
    rsync -av /tmp/backup/current/ /var/lib/postgresql/12/main
    # Touch a recovery file
    touch /var/lib/postgresql/12/main/recovery.signal
    
    # As $username (with sudo right)
    sudo vim /usr/share/postgresql-common/t/12.conf
    # restore_command = 'cp "/tmp/backup/wal_archive/%f" "%p"'
    sudo systemctl restart postgresql
    sudo systemctl status postgresql
    # ● postgresql.service - PostgreSQL RDBMS
    #      Loaded: loaded (/lib/systemd/system/postgresql.service; enabled; vendor preset: enabled)
    #      Active: active (exited) since Fri 2022-12-02 20:46:37 CET; 3s ago
    #     Process: 89096 ExecStart=/bin/true (code=exited, status=0/SUCCESS)
    #    Main PID: 89096 (code=exited, status=0/SUCCESS)
    
    # Dec 02 20:46:37 svvm0147 systemd[1]: Starting PostgreSQL RDBMS...
    # Dec 02 20:46:37 svvm0147 systemd[1]: Finished PostgreSQL RDBMS.
    
    # As postgres user:
    psql 
    # psql: error: could not connect to server: No such file or directory
    #         Is the server running locally and accepting
    #         connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?
    Lucille Delisle
    @lldelisle
    I think I managed. Sorry for all the noise.
    1 reply
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    is there an issue with testtoolshed? I'm getting a 500 on trying to shed_update lukasa:
    Could not update lukasa
    Unexpected HTTP status code: 500: <html>
      <head><title>Internal Server Error</title></head>
      <body>
        <h1>Internal Server Error</h1>
        <p>The server has either erred or is incapable of performing
    the requested operation.
    
    <br/>
    <!--  --></p>
        <hr noshade>
        <div align="right">WSGI Server</div>
      </body>
    </html>
    Marius
    @mvdbeek:matrix.org
    [m]
    It's not restarting automatically anymore when reaching a certain memory level, I think that's your issue
    I'll let you know when it's fixed up
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    is the testtoolshed still having problems with updates?
    1 reply
    Helena
    @hexylena:matrix.org
    [m]
    Without any other modifications, just addition of SCRIPT_NAME needed.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    yes that looks like a likely candidate for what is going on here... Nate Coraor has the testtoolshed code been updated recently?
    Lucille Delisle
    @lldelisle
    Yes we did with @mvdbeek:matrix.org
    But this was November 4th...
    Lucille Delisle
    @lldelisle
    This is what we changed: galaxyproject/galaxy@a02d407
    I don't know if that explains
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    agreed. that doesn't seem to be related to this problem. Marius seemed to think it was a memory problem the other day
    Also I remember that I updated a tool after updating the testtoolshed and it worked.
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    works for me too
    Peter Cock
    @peterjc
    It looks like planemo shed_update is now working, but not with --show_diff. Nor is planemo shed_diffworking for me:
    $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/ -m "v0.3.0  - Updated to BLAST+ 2.9.0 via conda; removed legacy tool packages."
    cd '/Users/pc40583/repositories/galaxy_blast/tools/blast_rbh' && git rev-parse HEAD
    galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
    git diff --quiet
    Diffing repository [blast_rbh]
    tar -C /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tool_shed_diff_08k1lg9a/_testtoolshed_ -xzf - --strip-components=1
    tar: Error opening archive: Unrecognized archive format
    tar -xzf /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tmpw8vt881y -C /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tool_shed_diff_08k1lg9a/_workingdir_
    diff -r _workingdir_ _testtoolshed_
    Only in _workingdir_: test-data
    Only in _workingdir_: tools
    Repository blast_rbh updated successfully.
    Repository metadata updated successfully for repository 'blast_rbh' on the test Tool Shed.
    $ planemo shed_diff -t testtoolshed tools/blast_rbh/
    Diffing repository [blast_rbh]
    tar -C /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tool_shed_diff_8kds1pph/_testtoolshed_ -xzf - --strip-components=1
    tar: Error opening archive: Unrecognized archive format
    tar -xzf /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tmp5g9zwgbw -C /var/folders/xq/zhs3hy7x5cv50svc4s7q2_9h0000gn/T/tool_shed_diff_8kds1pph/_workingdir_
    diff -r _workingdir_ _testtoolshed_
    Only in _workingdir_: test-data
    Only in _workingdir_: tools
    Marius
    @mvdbeek:matrix.org
    [m]
    Don't assume that the testtoolshed works at all times, like test.galaxyproject.org this is our testing ground, and I think we're a little strapped in admin time to guarantee speedy fixes here. Like I said, for some reason systemd doesn't apply the memory limit, so then all bets are off to what works
    that's not the same for the main toolshed, if something's wrong there we'll obviously fix it asap
    Peter Cock
    @peterjc
    Thanks - I appreciate it gets used for testing both sides of the system, I've held off pushing my riskier changes to the main Tool Shed in the interim - want to see the planned packaging changes actually work first ;)
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    Marius understood, but as a tool developer I try to not "pollute" the main toolshed with experimental code. With running a local toolshed being discouraged it kind of begs the question of what one should be using for experimentation
    Marius
    @mvdbeek:matrix.org
    [m]
    I don't have an answer, I can only tell you why things aren't working right now
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    :) thanks
    Helena
    @hexylena:matrix.org
    [m]

    some ansible things I didn't know before:

    ansible-doc let's you access module docs, without a web browser. That'll save me having 30 tabs open for module docs like copy and so on. Just ansible-doc copy and you can see docs/examples/etc.

    ansible-navigator, maybe interesting for others. (warning, pulls a docker image.), it's realyl an ansible tui